From c8a06e53c17cb4a4c8d2e76f2ae24aa32ccbd6ae Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sat, 25 Feb 2012 11:32:50 -0500 Subject: [PATCH] DoC now properly handles reference N bases + misc. additional cleanups -- DoC now by default ignores bases with reference Ns, so these are not included in the coverage calculations at any stage. -- Added option --includeRefNSites that will include them in the calculation -- Added integration tests that ensures the per base tables (and so all subsequent calculations) work with and without reference N bases included -- Reorganized command line options, tagging advanced options with @Advanced --- .../coverage/DepthOfCoverageWalker.java | 107 ++++++++++++------ .../DepthOfCoverageIntegrationTest.java | 10 ++ 2 files changed, 80 insertions(+), 37 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index cbbb3d43f..7d1858a63 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage; import net.sf.samtools.SAMReadGroupRecord; +import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -119,21 +120,6 @@ public class DepthOfCoverageWalker extends LocusWalker out; - /** - * Sets the low-coverage cutoff for granular binning. All loci with depth < START are counted in the first bin. - */ - @Argument(fullName = "start", doc = "Starting (left endpoint) for granular binning", required = false) - int start = 1; - /** - * Sets the high-coverage cutoff for granular binning. All loci with depth > END are counted in the last bin. - */ - @Argument(fullName = "stop", doc = "Ending (right endpoint) for granular binning", required = false) - int stop = 500; - /** - * Sets the number of bins for granular binning - */ - @Argument(fullName = "nBins", doc = "Number of bins to use for granular binning", required = false) - int nBins = 499; @Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to -1.", required = false) int minMappingQuality = -1; @Argument(fullName = "maxMappingQuality", doc = "Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).", required = false) @@ -142,16 +128,19 @@ public class DepthOfCoverageWalker extends LocusWalker END are counted in the last bin. + */ + @Advanced + @Argument(fullName = "stop", doc = "Ending (right endpoint) for granular binning", required = false) + int stop = 500; + /** + * Sets the number of bins for granular binning + */ + @Advanced + @Argument(fullName = "nBins", doc = "Number of bins to use for granular binning", required = false) + int nBins = 499; + /** * Do not tabulate the sample summary statistics (total, mean, median, quartile coverage per sample) */ @@ -174,27 +207,22 @@ public class DepthOfCoverageWalker extends LocusWalker partitionTypes = EnumSet.of(DoCOutputType.Partition.sample); + /** * Consider a spanning deletion as contributing to coverage. Also enables deletion counts in per-base output. */ + @Advanced @Argument(fullName = "includeDeletions", shortName = "dels", doc = "Include information on deletions", required = false) boolean includeDeletions = false; + + @Advanced @Argument(fullName = "ignoreDeletionSites", doc = "Ignore sites consisting only of deletions", required = false) boolean ignoreDeletionSites = false; - /** - * Path to the RefSeq file for use in aggregating coverage statistics over genes - */ - @Argument(fullName = "calculateCoverageOverGenes", shortName = "geneList", doc = "Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.", required = false) - File refSeqGeneList = null; - /** - * The format of the output file - */ - @Argument(fullName = "outputFormat", doc = "the format of the output file (e.g. csv, table, rtable); defaults to r-readable table", required = false) - String outputFormat = "rtable"; /** * A coverage threshold for summarizing (e.g. % bases >= CT for each sample) */ + @Advanced @Argument(fullName = "summaryCoverageThreshold", shortName = "ct", doc = "for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.", required = false) int[] coverageThresholds = {15}; @@ -334,24 +362,29 @@ public class DepthOfCoverageWalker extends LocusWalker> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if (includeRefNBases || BaseUtils.isRegularBase(ref.getBase())) { + if ( ! omitDepthOutput ) { + getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary).printf("%s",ref.getLocus()); // yes: print locus in map, and the rest of the info in reduce (for eventual cumulatives) + //System.out.printf("\t[log]\t%s",ref.getLocus()); + } - if ( ! omitDepthOutput ) { - getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary).printf("%s",ref.getLocus()); // yes: print locus in map, and the rest of the info in reduce (for eventual cumulatives) - //System.out.printf("\t[log]\t%s",ref.getLocus()); + return CoverageUtils.getBaseCountsByPartition(context,minMappingQuality,maxMappingQuality,minBaseQuality,maxBaseQuality,partitionTypes); + } else { + return null; } - - return CoverageUtils.getBaseCountsByPartition(context,minMappingQuality,maxMappingQuality,minBaseQuality,maxBaseQuality,partitionTypes); } public CoveragePartitioner reduce(Map> thisMap, CoveragePartitioner prevReduce) { - if ( ! omitDepthOutput ) { - //checkOrder(prevReduce); // tests prevReduce.getIdentifiersByType().get(t) against the initialized header order - printDepths(getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary),thisMap,prevReduce.getIdentifiersByType()); - // this is an additional iteration through thisMap, plus dealing with IO, so should be much slower without - // turning on omit - } + if ( thisMap != null ) { // skip sites we didn't want to include in the calculation (ref Ns) + if ( ! omitDepthOutput ) { + //checkOrder(prevReduce); // tests prevReduce.getIdentifiersByType().get(t) against the initialized header order + printDepths(getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary),thisMap,prevReduce.getIdentifiersByType()); + // this is an additional iteration through thisMap, plus dealing with IO, so should be much slower without + // turning on omit + } - prevReduce.update(thisMap); // note that in "useBoth" cases, this method alters the thisMap object + prevReduce.update(thisMap); // note that in "useBoth" cases, this method alters the thisMap object + } return prevReduce; } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java index 1c58346b4..6f1370008 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java @@ -94,4 +94,14 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { execute("testNoCoverageDueToFiltering",spec); } + + public void testRefNHandling(boolean includeNs, final String md5) { + String command = "-R " + b37KGReference + " -L 20:26,319,565-26,319,575 -I " + validationDataLocation + "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -T DepthOfCoverage -baseCounts --omitIntervalStatistics --omitLocusTable --omitPerSampleStats -o %s"; + if ( includeNs ) command += " --includeRefNSites"; + WalkerTestSpec spec = new WalkerTestSpec(command, 1, Arrays.asList(md5)); + executeTest("Testing DoC " + (includeNs ? "with" : "without") + " reference Ns", spec); + } + + @Test public void testRefNWithNs() { testRefNHandling(true, "24cd2da2e4323ce6fd76217ba6dc2834"); } + @Test public void testRefNWithoutNs() { testRefNHandling(false, "4fc0f1a2e968f777d693abcefd4fb7af"); } }